`run_pairwise_tests`¶

Runs all pairwise RAISIN contrasts for the groups in a fitted model and generates the volcano plots, per-pair results CSVs, and summary figures. Internally calls raisintest once per pair (or once per non-control group when control_group is set) and aggregates the outputs into a summary_plots/ folder with a cross-cluster pseudobulk heatmap and a summary dotplot of DE gene counts.

Source: sampledisco/sample_clustering/RAISIN_TEST.py:609

Signature¶

def run_pairwise_tests(
    fit,
    output_dir,
    groups_to_compare=None,
    control_group=None,
    fdrmethod="fdr_bh",
    n_permutations=100,
    fdr_threshold=0.05,
    top_n_genes: int = 50,
    make_summary_plots: bool = True,
    verbose=True,
    random_state: int = 42,
)

Parameters¶

Name	Type	Default	Description
`fit`	dict	—	Output of `raisinfit`.
`output_dir`	str	—	Writes to `{output_dir}/{group1}_vs_{group2}/` for each pair plus `{output_dir}/summary_plots/`.
`groups_to_compare`	list, optional	`None`	Subset of groups to consider. Defaults to all groups in `fit["group"]`.
`control_group`	str, optional	`None`	If set, tests every other group against this reference rather than all pairwise combinations.
`fdrmethod`	str	`"fdr_bh"`	statsmodels multi-testing method.
`n_permutations`	int	`100`	Number of permutations used by `raisintest` for empirical calibration.
`fdr_threshold`	float	`0.05`	Cutoff used when drawing volcano significance bands and counting DE genes.
`top_n_genes`	int	`50`	How many top genes to annotate in the volcano and heatmap.
`make_summary_plots`	bool	`True`	Emit `summary_plots/pseudobulk_heatmap.png`, `summary_plots/summary_dotplot.png`, `summary_plots/cluster_gene_zscore.png`.
`verbose`	bool	`True`	Print progress.
`random_state`	int	`42`	Seed passed to `raisintest` for the permutation calibration of each pair.

Returns¶

(results_summary, all_results) — a 2-tuple. results_summary is a dict mapping each {group1}_vs_{group2} comparison to its count of significant genes (FDR < fdr_threshold); all_results is a dict mapping each comparison to its per-pair RAISIN results DataFrame. The function also writes the per-pair CSVs/PNGs and the summary folder described below.

Output files¶

Per pair:

{group1}_vs_{group2}/raisin_results.csv
{group1}_vs_{group2}/volcano.png
{group1}_vs_{group2}/volcano_labeled.png

Across all pairs (a summary_plots/ folder is always written; the PNG plots require make_summary_plots=True):

summary_plots/raisin_summary.csv
summary_plots/raisin_summary.txt
summary_plots/pseudobulk_heatmap.png
summary_plots/summary_dotplot.png
summary_plots/cluster_gene_zscore.png
summary_plots/all_results_combined.csv

Usage¶

from sampledisco.sample_clustering.RAISIN_TEST import run_pairwise_tests

results_summary, all_results = run_pairwise_tests(
    fit=fit,
    output_dir="sampledisco_demo_output/rna/raisin_results",
    groups_to_compare=None,
    control_group=None,
    fdr_threshold=0.05,
    top_n_genes=50,
    make_summary_plots=True,
)

run_pairwise_tests¶